Maj. General Benjamin Lincoln returned to duty in August 1778. He rejoined General George Washington's main army. He offered his resignation over the controversy now created by Benedict Arnold over promotions, but he was convinced to remain in service. On September 25, 1778, he was appointed by Congress to replace Maj. General Robert Howe as Southern Department Commander. After being delaying in Philadelphia by Congress, he did not arrive in Charleston, South Carolina until December 4, 1778. The timing of his arrival made him unable to prevent the capture of Savannah, Georgia on December 29th.

When he arrived, Lincoln's force numbered 1,121 Continental troops and 2,518 militia, of which 2,428 troops were fit for duty. Soon after his arrival, Lincoln shored up a position south of Charleston to protect it from being captured by General Augustine Prevost, a Swiss mercenary serving in the British Army. Meanwhile, Lt. Colonel Archibald Campbell marched virtually unopposed against Augusta, Georgia, occupying it on January 29, 1779. An advance force sent by Prevost was rebuffed by Brig. General William Moultrie at Beauford (Port Royal Island), South Carolina on February 2, 1779.

General Moultrie's victory helped bolster Lincoln's ranks with additional militia, so he undertook a counteroffensive to regain Georgia. The British evacuated Augusta, Georgia, while Andrew Pickens was victorious at Kettle Creek, Georgia on February 14, 1779. However, the counteroffensive stalled when a 1,500 man force under Brig. General John Ashe was destroyed at Briar Creek, Georgia on March 3rd. This was followed by an advance by General Prevost against Charleston. Lincoln was forced to retreat back to Charleston to protect the city.

The oppressive heat of the summer months halted major operations for both sides for several month. Lincoln spent this time appealing to French Admiral Count d'Estaing to sail from the West Indies and join in the efforts to recapture Georgia. In September 1779, d'Estaing arrived to the complete surprise of the British. On October 9, Lincoln was joined by French troops and d'Estaing's fleet in an assault on Savannah, which was rebuffed. Although Lincoln pleaded to continue the siege, the French abandoned the offensive on October 20th. Lincoln then retreated back to Charleston.

In February 1780, Lt. General Henry Clinton arrived leading a large expedition with the purpose of subjugating the Southern colonies. Charleston's greatest asset was its harbor, which had been defended effectively at the Battle of Fort Sullivan on June 28, 1776. Lincoln relied on Commodore Abraham Whipple's expertise for protecting Charleston Harbor in the face of this new assault. Whipple gave up defense of the harbor without a fight and the British easily secured use of the waterways around Charleston. Lincoln was left with little to do, but watch as the British slowly closed in. After a month long seige by the British, Lincoln surrendered on May 12, 1780.